Sullivan leads Begich by 49 percent to 45 percent with 100 percent of precincts reporting. The Associated Press has not called the race, and Begich has not conceded.

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Sullivan ran a disciplined campaign, posting huge fundraising numbers and relentlessly tying Begich to President Obama, as he attacked government regulation.

He managed to unite a fractured Republican base, boosted by the endorsements of his primary foes 2010 Senate nominee Joe Miller (R) and outgoing Alaska Lt. Gov. Mead Treadwell (R). He also got a big boost with centrists and independents from Sen. Lisa Murkowski (R-Alaska), who gave him a hearty endorsement and fought with Begich throughout the campaign.

Begich ran hard on centrist credentials, highlighting his splits from Obama on energy production, gun control and other issues. But it appears that he couldn't get enough distance from the president on a terrible night for his party and in the heavily Republican state.

Begich isn't conceding, arguing that the outstanding rural vote could help him close the gap. Begich's campaign has long been predicated big wins in rural Alaska, which has large populations of Native Alaskans.

"From Southeast Alaska to the North Slope, every Alaskan deserves to have their vote counted," Begich campaign manager Susanne Fleek-Green said in a statement Wednesday morning. "Senator Begich is proud to have run the most extensive campaign in rural Alaska's history and to have stood for the rights of Alaska Natives and rural Alaska. Begich will make a statement on the race after counts arrive from the seventy outstanding villages and when the number of outstanding absentee and questioned ballots is clear."

— This report was originally published at 4:07 a.m. and last updated at 6:44 a.m.